0s autopkgtest [21:15:55]: starting date and time: 2025-03-15 21:15:55+0000 0s autopkgtest [21:15:55]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:15:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.80tbty1q/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade physamp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-18.secgroup --name adt-plucky-amd64-physamp-20250315-211554-juju-7f2275-prod-proposed-migration-environment-2-166de6a2-b886-45ca-a44c-2457749262f3 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 48s autopkgtest [21:16:43]: testbed dpkg architecture: amd64 48s autopkgtest [21:16:43]: testbed apt version: 2.9.31ubuntu1 48s autopkgtest [21:16:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s autopkgtest [21:16:44]: testbed release detected to be: None 49s autopkgtest [21:16:44]: updating testbed package index (apt update) 50s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 50s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 50s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 50s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 50s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 50s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 50s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 50s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 50s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 50s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 50s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 50s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 50s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 50s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 50s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 50s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 51s Fetched 1265 kB in 1s (1466 kB/s) 52s Reading package lists... 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Calculating upgrade... 53s Calculating upgrade... 53s The following package was automatically installed and is no longer required: 53s libnl-genl-3-200 53s Use 'sudo apt autoremove' to remove it. 53s The following NEW packages will be installed: 53s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 53s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 53s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 53s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 53s The following packages will be upgraded: 53s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 53s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 53s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 53s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 53s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 53s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 53s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 53s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 54s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 54s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 54s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 54s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 54s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 54s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 54s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 54s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 54s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 54s parted pci.ids pciutils pinentry-curses python-apt-common python3 54s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 54s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 54s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 54s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 54s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 54s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 54s xz-utils 54s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 829 MB of archives. 54s After this operation, 325 MB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 54s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 54s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 54s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 54s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 54s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 54s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 54s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 54s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 54s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 54s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 54s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 54s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 54s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 54s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 55s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 55s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 55s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 55s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 55s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 55s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 55s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 55s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 55s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 55s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 55s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 55s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 55s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 55s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 55s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 55s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 55s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 55s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 55s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 55s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 55s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 55s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 55s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 55s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 55s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 55s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 55s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 55s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 55s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 55s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 55s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 55s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 55s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 55s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 55s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 55s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 55s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 55s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 55s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 55s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 55s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 55s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 55s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 55s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 55s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 55s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 55s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 55s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 55s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 55s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 55s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 55s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 55s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 55s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 55s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 55s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 56s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 56s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 56s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 56s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 56s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 56s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 56s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 56s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 56s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 56s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 56s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 56s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 56s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 56s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 56s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 56s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 56s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 56s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 56s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 56s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 56s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 56s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 56s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 56s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 56s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 56s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 56s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 56s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 56s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 56s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 56s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 56s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 56s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 57s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 57s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 57s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 57s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 57s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 83s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 83s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 83s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 83s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 83s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 83s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 83s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 83s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 84s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 85s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 92s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 92s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 92s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 92s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 92s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 92s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 93s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 93s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 93s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 93s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 93s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 93s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 93s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 93s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 93s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 93s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 93s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 93s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 93s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 94s Preconfiguring packages ... 94s Fetched 829 MB in 40s (20.9 MB/s) 94s (Reading database ... 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.../23-parted_3.6-5_amd64.deb ... 106s Unpacking parted (3.6-5) over (3.6-4build1) ... 106s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 106s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 106s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 106s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 106s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 106s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 106s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 106s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 106s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 106s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 106s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 106s Unpacking strace 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new version of config file /etc/mime.types ... 120s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 120s Setting up ubuntu-kernel-accessories (1.549) ... 120s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 120s Setting up pci.ids (0.0~2025.03.09-1) ... 120s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 120s Setting up apt-utils (2.9.33) ... 120s Setting up libdebuginfod-common (0.192-4) ... 120s Setting up exfatprogs (1.2.8-1) ... 120s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 120s Setting up bpftool (7.6.0+6.14.0-10.10) ... 120s Setting up libestr0:amd64 (0.1.11-2) ... 120s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 120s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 120s Setting up dosfstools (4.2-1.2) ... 120s Setting up rsyslog (8.2412.0-2ubuntu2) ... 120s info: The user `syslog' is already a member of `adm'. 121s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 121s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 121s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 121s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 121s Setting up systemd (257.3-1ubuntu3) ... 121s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 121s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 122s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 122s Setting up libparted2t64:amd64 (3.6-5) ... 122s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 122s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 122s Setting up linux-headers-generic (6.14.0-10.10) ... 122s Setting up libjemalloc2:amd64 (5.3.0-3) ... 122s Setting up locales (2.41-1ubuntu1) ... 122s Installing new version of config file /etc/locale.alias ... 123s Generating locales (this might take a while)... 124s en_US.UTF-8... done 124s Generation complete. 124s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 124s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 124s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 124s Installing new version of config file /etc/apparmor.d/fusermount3 ... 124s Installing new version of config file /etc/apparmor.d/lsusb ... 124s Installing new version of config file /etc/apparmor.d/openvpn ... 126s Reloading AppArmor profiles 127s Setting up libftdi1-2:amd64 (1.5-8build1) ... 127s Setting up libglib2.0-data (2.84.0-1) ... 127s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 127s Setting up libncurses6:amd64 (6.5+20250216-2) ... 127s Setting up strace (6.13+ds-1ubuntu1) ... 127s Setting up xz-utils (5.6.4-1) ... 127s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 128s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 128s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 128s Setting up udev (257.3-1ubuntu3) ... 129s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 131s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 131s Setting up libpci3:amd64 (1:3.13.0-2) ... 131s Setting up whiptail (0.52.24-4ubuntu2) ... 131s Setting up python-apt-common (2.9.9build1) ... 131s Setting up pnp.ids (0.393-3) ... 131s Setting up libnl-3-200:amd64 (3.7.0-1) ... 131s Setting up python3.13-minimal (3.13.2-2) ... 131s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 131s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 131s Setting up libc-dev-bin (2.41-1ubuntu1) ... 131s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 131s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 131s Setting up rsync (3.4.1+ds1-3) ... 132s rsync.service is a disabled or a static unit not running, not starting it. 132s Setting up python3.13-gdbm (3.13.2-2) ... 132s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 132s Setting up systemd-resolved (257.3-1ubuntu3) ... 133s Setting up initramfs-tools-bin (0.146ubuntu1) ... 133s Setting up ncurses-term (6.5+20250216-2) ... 133s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 133s Setting up libpython3.13:amd64 (3.13.2-2) ... 133s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 133s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 133s Setting up systemd-sysv (257.3-1ubuntu3) ... 133s Setting up linux-headers-virtual (6.14.0-10.10) ... 133s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 133s Setting up python3.13 (3.13.2-2) ... 134s Setting up htop (3.4.0-2) ... 134s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 136s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 136s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 136s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 136s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 136s Setting up parted (3.6-5) ... 136s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 136s Setting up python3 (3.13.2-2) ... 136s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 136s Setting up python3-markupsafe (2.1.5-1build4) ... 136s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 138s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 138s Setting up hwdata (0.393-3) ... 138s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 139s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 139s No schema files found: doing nothing. 139s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 139s Setting up linux-perf (6.14.0-10.10) ... 139s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 139s Setting up pciutils (1:3.13.0-2) ... 139s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 139s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 139s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 139s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 139s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 139s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 139s Setting up curl (8.12.1-3ubuntu1) ... 139s Setting up linux-image-virtual (6.14.0-10.10) ... 139s Setting up initramfs-tools-core (0.146ubuntu1) ... 139s Setting up linux-tools-common (6.14.0-10.10) ... 139s Setting up python3-systemd (235-1build6) ... 139s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 139s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 139s Setting up linux-image-generic (6.14.0-10.10) ... 139s Setting up python3-dbus (1.3.2-5build5) ... 139s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 139s Setting up initramfs-tools (0.146ubuntu1) ... 139s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 139s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 139s update-initramfs: deferring update (trigger activated) 139s Setting up linux-generic (6.14.0-10.10) ... 139s Setting up ubuntu-minimal (1.549) ... 139s Setting up python3-apt (2.9.9build1) ... 139s Setting up python3-bcrypt (4.2.0-2.1build1) ... 139s Setting up python3-yaml (6.0.2-1build2) ... 140s Setting up libfwupd3:amd64 (2.0.6-4) ... 140s Setting up python3-lazr.uri (1.0.6-6) ... 140s Setting up binutils (2.44-3ubuntu1) ... 140s Setting up ubuntu-standard (1.549) ... 140s Setting up cloud-init-base (25.1-0ubuntu3) ... 141s Setting up linux-virtual (6.14.0-10.10) ... 141s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 141s Setting up python3-gi (3.50.0-4build1) ... 141s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 141s Setting up fwupd (2.0.6-4) ... 142s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 142s Setting up cloud-init (25.1-0ubuntu3) ... 142s Processing triggers for man-db (2.13.0-1) ... 144s Processing triggers for dbus (1.16.2-1ubuntu1) ... 144s Processing triggers for shared-mime-info (2.4-5) ... 144s Warning: program compiled against libxml 212 using older 209 145s Processing triggers for libc-bin (2.41-1ubuntu1) ... 145s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 145s /etc/kernel/postinst.d/initramfs-tools: 145s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 145s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 155s /etc/kernel/postinst.d/zz-update-grub: 155s Sourcing file `/etc/default/grub' 155s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 155s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 155s Generating grub configuration file ... 155s Found linux image: /boot/vmlinuz-6.14.0-10-generic 155s Found initrd image: /boot/initrd.img-6.14.0-10-generic 156s Found linux image: /boot/vmlinuz-6.12.0-16-generic 156s Found initrd image: /boot/initrd.img-6.12.0-16-generic 156s Found linux image: /boot/vmlinuz-6.11.0-8-generic 156s Found initrd image: /boot/initrd.img-6.11.0-8-generic 156s Warning: os-prober will not be executed to detect other bootable partitions. 156s Systems on them will not be added to the GRUB boot configuration. 156s Check GRUB_DISABLE_OS_PROBER documentation entry. 156s Adding boot menu entry for UEFI Firmware Settings ... 156s done 156s Processing triggers for initramfs-tools (0.146ubuntu1) ... 156s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 156s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 169s Solving dependencies... 169s The following packages will be REMOVED: 169s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 169s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 169s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 169s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 169s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 169s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 169s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 169s linux-tools-6.12.0-16-generic* 169s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 169s After this operation, 545 MB disk space will be freed. 169s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 148643 files and directories currently installed.) 169s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 169s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 169s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 169s Removing libpython3.12t64:amd64 (3.12.9-1) ... 169s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 170s Removing libnsl2:amd64 (1.3.0-3build3) ... 170s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 170s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 170s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 172s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 173s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 175s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 175s /etc/kernel/postrm.d/initramfs-tools: 175s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 176s /etc/kernel/postrm.d/zz-update-grub: 176s Sourcing file `/etc/default/grub' 176s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 176s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 176s Generating grub configuration file ... 176s Found linux image: /boot/vmlinuz-6.14.0-10-generic 176s Found initrd image: /boot/initrd.img-6.14.0-10-generic 176s Found linux image: /boot/vmlinuz-6.12.0-16-generic 176s Found initrd image: /boot/initrd.img-6.12.0-16-generic 176s Warning: os-prober will not be executed to detect other bootable partitions. 176s Systems on them will not be added to the GRUB boot configuration. 176s Check GRUB_DISABLE_OS_PROBER documentation entry. 176s Adding boot menu entry for UEFI Firmware Settings ... 176s done 176s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 177s W: Removing the running kernel 177s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 177s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 177s /etc/kernel/postrm.d/initramfs-tools: 177s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 177s /etc/kernel/postrm.d/zz-update-grub: 177s Sourcing file `/etc/default/grub' 177s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 177s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 177s Generating grub configuration file ... 177s Found linux image: /boot/vmlinuz-6.14.0-10-generic 177s Found initrd image: /boot/initrd.img-6.14.0-10-generic 177s Warning: os-prober will not be executed to detect other bootable partitions. 177s Systems on them will not be added to the GRUB boot configuration. 177s Check GRUB_DISABLE_OS_PROBER documentation entry. 177s Adding boot menu entry for UEFI Firmware Settings ... 177s done 177s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 177s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 179s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 179s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 179s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 179s Processing triggers for libc-bin (2.41-1ubuntu1) ... 179s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76972 files and directories currently installed.) 179s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 179s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 180s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 180s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 180s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 180s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 180s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 180s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 180s autopkgtest [21:18:55]: upgrading testbed (apt dist-upgrade and autopurge) 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 181s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 182s Entering ResolveByKeep 182s 182s Calculating upgrade... 182s The following packages will be upgraded: 182s libc-bin libc-dev-bin libc6 libc6-dev locales 182s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s Need to get 10.5 MB of archives. 182s After this operation, 1024 B of additional disk space will be used. 182s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 183s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 183s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 183s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 184s Preconfiguring packages ... 184s Fetched 10.5 MB in 1s (7654 kB/s) 184s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 184s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 184s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 184s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 184s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 184s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 184s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 184s Setting up libc6:amd64 (2.41-1ubuntu2) ... 185s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 185s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 185s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 185s Setting up libc-bin (2.41-1ubuntu2) ... 185s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 185s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 185s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 185s Setting up locales (2.41-1ubuntu2) ... 186s Generating locales (this might take a while)... 187s en_US.UTF-8... done 187s Generation complete. 187s Setting up libc-dev-bin (2.41-1ubuntu2) ... 187s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 187s Processing triggers for man-db (2.13.0-1) ... 188s Processing triggers for systemd (257.3-1ubuntu3) ... 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 190s Solving dependencies... 190s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s autopkgtest [21:19:05]: rebooting testbed after setup commands that affected boot 213s autopkgtest [21:19:28]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 216s autopkgtest [21:19:31]: @@@@@@@@@@@@@@@@@@@@ apt-source physamp 218s Get:1 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (dsc) [2001 B] 218s Get:2 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (tar) [242 kB] 218s Get:3 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (diff) [3924 B] 219s gpgv: Signature made Mon Mar 25 18:00:09 2024 UTC 219s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./physamp_1.1.0-5.dsc: no acceptable signature found 219s autopkgtest [21:19:34]: testing package physamp version 1.1.0-5 219s autopkgtest [21:19:34]: build not needed 220s autopkgtest [21:19:35]: test run-unit-test: preparing testbed 220s Reading package lists... 220s Building dependency tree... 220s Reading state information... 220s Starting pkgProblemResolver with broken count: 0 220s Starting 2 pkgProblemResolver with broken count: 0 220s Done 221s The following NEW packages will be installed: 221s libbpp-core4t64 libbpp-phyl12t64 libbpp-seq12t64 physamp 221s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 221s Need to get 3277 kB of archives. 221s After this operation, 18.1 MB of additional disk space will be used. 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbpp-core4t64 amd64 2.4.1-13 [667 kB] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbpp-seq12t64 amd64 2.4.1-13 [545 kB] 222s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbpp-phyl12t64 amd64 2.4.1-9.1ubuntu3 [1887 kB] 222s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 physamp amd64 1.1.0-5 [178 kB] 222s Fetched 3277 kB in 1s (4470 kB/s) 222s Selecting previously unselected package libbpp-core4t64:amd64. 222s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 76968 files and directories currently installed.) 222s Preparing to unpack .../libbpp-core4t64_2.4.1-13_amd64.deb ... 222s Unpacking libbpp-core4t64:amd64 (2.4.1-13) ... 222s Selecting previously unselected package libbpp-seq12t64:amd64. 222s Preparing to unpack .../libbpp-seq12t64_2.4.1-13_amd64.deb ... 222s Unpacking libbpp-seq12t64:amd64 (2.4.1-13) ... 222s Selecting previously unselected package libbpp-phyl12t64:amd64. 222s Preparing to unpack .../libbpp-phyl12t64_2.4.1-9.1ubuntu3_amd64.deb ... 222s Unpacking libbpp-phyl12t64:amd64 (2.4.1-9.1ubuntu3) ... 223s Selecting previously unselected package physamp. 223s Preparing to unpack .../physamp_1.1.0-5_amd64.deb ... 223s Unpacking physamp (1.1.0-5) ... 223s Setting up libbpp-core4t64:amd64 (2.4.1-13) ... 223s Setting up libbpp-seq12t64:amd64 (2.4.1-13) ... 223s Setting up libbpp-phyl12t64:amd64 (2.4.1-9.1ubuntu3) ... 223s Setting up physamp (1.1.0-5) ... 223s Processing triggers for man-db (2.13.0-1) ... 223s Processing triggers for install-info (7.1.1-1) ... 224s Processing triggers for libc-bin (2.41-1ubuntu2) ... 225s autopkgtest [21:19:40]: test run-unit-test: [----------------------- 225s ****************************************************************** 225s * Bio++ Alignment Optimizer, version 1.1.0. * 225s * Author: J. Dutheil Last Modif. 14/03/18 * 225s * E. Figuet * 225s ****************************************************************** 225s 225s Parsing options: 225s Parsing file AlnOptimFasttree.bpp for options. 225s Alphabet type .........................: Proteic 225s Sequence file .........................: PF01049_full.txt 225s Sequence format .......................: FASTA file 225s Minimum amount of data per site........: 0.7 225s Filter gap characters..................: yes 225s Filter unresolved characters...........: yes 225s Number of reference sequences..........: 0 225s Total number of sequences..............: 1652 225s Total number of sites..................: 656 225s Input tree file .......................: PF01049_fasttree.dnd 225s Input tree format .....................: Newick 225s Comparison criterion:..................: MaxSites 225s Number of sequences in alignment.......: 1652 225s Number of sites in alignment...........: 129 225s Number of chars in alignment...........: 182603 225s Mean site entropy in alignment.........: 0.394104 225s Choice Node #seq %seq #sites %sites #chars %chars 225s 1) 2030 1647 -5 131 +2 184714 2111 225s Number of sequences in alignment.......: 1647 225s Number of sites in alignment...........: 131 225s Number of chars in alignment...........: 184714 225s Mean site entropy in alignment.........: 0.394129 225s Choice Node #seq %seq #sites %sites #chars %chars 225s 1) 1930 1645 -2 132 +1 185794 1080 225s Number of sequences in alignment.......: 1645 225s Number of sites in alignment...........: 132 225s Number of chars in alignment...........: 185794 225s Mean site entropy in alignment.........: 0.394195 225s Choice Node #seq %seq #sites %sites #chars %chars 225s 1) 1882 1644 -1 133 +1 186920 1126 226s Number of sequences in alignment.......: 1644 226s Number of sites in alignment...........: 133 226s Number of chars in alignment...........: 186920 226s Mean site entropy in alignment.........: 0.394263 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 386 1634 -10 134 +1 187634 714 226s Number of sequences in alignment.......: 1634 226s Number of sites in alignment...........: 134 226s Number of chars in alignment...........: 187634 226s Mean site entropy in alignment.........: 0.394887 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 357 1627 -7 135 +1 188437 803 226s Number of sequences in alignment.......: 1627 226s Number of sites in alignment...........: 135 226s Number of chars in alignment...........: 188437 226s Mean site entropy in alignment.........: 0.394741 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 1736 1614 -13 136 +1 188713 276 226s Number of sequences in alignment.......: 1614 226s Number of sites in alignment...........: 136 226s Number of chars in alignment...........: 188713 226s Mean site entropy in alignment.........: 0.394145 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 1489 1527 -87 137 +1 181488 -7225 226s Number of sequences in alignment.......: 1527 226s Number of sites in alignment...........: 137 226s Number of chars in alignment...........: 181488 226s Mean site entropy in alignment.........: 0.378687 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 2247 1524 -3 138 +1 182435 947 226s Number of sequences in alignment.......: 1524 226s Number of sites in alignment...........: 138 226s Number of chars in alignment...........: 182435 226s Mean site entropy in alignment.........: 0.378731 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 408 1515 -9 139 +1 183008 573 226s Number of sequences in alignment.......: 1515 226s Number of sites in alignment...........: 139 226s Number of chars in alignment...........: 183008 226s Mean site entropy in alignment.........: 0.377294 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 1819 1488 -27 140 +1 182208 -800 226s Number of sequences in alignment.......: 1488 226s Number of sites in alignment...........: 140 226s Number of chars in alignment...........: 182208 226s Mean site entropy in alignment.........: 0.374188 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 1676 1464 -24 141 +1 180695 -1513 226s Number of sequences in alignment.......: 1464 226s Number of sites in alignment...........: 141 226s Number of chars in alignment...........: 180695 226s Mean site entropy in alignment.........: 0.371696 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 416 1457 -7 142 +1 181323 628 226s Number of sequences in alignment.......: 1457 226s Number of sites in alignment...........: 142 226s Number of chars in alignment...........: 181323 226s Mean site entropy in alignment.........: 0.36917 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 1823 1371 -86 143 +1 176415 -4908 226s Number of sequences in alignment.......: 1371 226s Number of sites in alignment...........: 143 226s Number of chars in alignment...........: 176415 226s Mean site entropy in alignment.........: 0.359961 226s Choice Node #seq %seq #sites %sites #chars %chars 226s 1) 783 1355 -16 144 +1 175237 -1178 227s Number of sequences in alignment.......: 1355 227s Number of sites in alignment...........: 144 227s Number of chars in alignment...........: 175237 227s Mean site entropy in alignment.........: 0.360644 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 953 1307 -48 145 +1 169472 -5765 227s Number of sequences in alignment.......: 1307 227s Number of sites in alignment...........: 145 227s Number of chars in alignment...........: 169472 227s Mean site entropy in alignment.........: 0.363152 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2269 476 -831 146 +1 66187 -103285 227s Number of sequences in alignment.......: 476 227s Number of sites in alignment...........: 146 227s Number of chars in alignment...........: 66187 227s Mean site entropy in alignment.........: 0.249565 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2488 413 -63 147 +1 57456 -8731 227s Number of sequences in alignment.......: 413 227s Number of sites in alignment...........: 147 227s Number of chars in alignment...........: 57456 227s Mean site entropy in alignment.........: 0.249617 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2372 411 -2 148 +1 57619 163 227s Number of sequences in alignment.......: 411 227s Number of sites in alignment...........: 148 227s Number of chars in alignment...........: 57619 227s Mean site entropy in alignment.........: 0.248169 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 179 391 -20 149 +1 55008 -2611 227s Number of sequences in alignment.......: 391 227s Number of sites in alignment...........: 149 227s Number of chars in alignment...........: 55008 227s Mean site entropy in alignment.........: 0.249151 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2697 54 -337 151 +2 7794 -47214 227s Number of sequences in alignment.......: 54 227s Number of sites in alignment...........: 151 227s Number of chars in alignment...........: 7794 227s Mean site entropy in alignment.........: 0.0871024 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2628 50 -4 152 +1 7230 -564 227s Number of sequences in alignment.......: 50 227s Number of sites in alignment...........: 152 227s Number of chars in alignment...........: 7230 227s Mean site entropy in alignment.........: 0.0864589 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2692 48 -2 153 +1 7110 -120 227s Number of sequences in alignment.......: 48 227s Number of sites in alignment...........: 153 227s Number of chars in alignment...........: 7110 227s Mean site entropy in alignment.........: 0.0765764 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2695 10 -38 154 +1 1526 -5584 227s Number of sequences in alignment.......: 10 227s Number of sites in alignment...........: 154 227s Number of chars in alignment...........: 1526 227s Mean site entropy in alignment.........: 0.0596881 227s Choice Node #seq %seq #sites %sites #chars %chars 227s 1) 2611 2 -8 156 +2 312 -1214 227s Number of sequences in alignment.......: 2 227s Number of sites in alignment...........: 156 227s Number of chars in alignment...........: 312 227s Mean site entropy in alignment.........: 0.0190193 227s Choice Node #seq %seq #sites %sites #chars %chars 227s BppAlnOpt's done. Bye. 227s Total execution time: 0.000000d, 0.000000h, 0.000000m, 2.000000s. 227s ****************************************************************** 227s * Bio++ Alignment Optimizer, version 1.1.0. * 227s * Author: J. Dutheil Last Modif. 14/03/18 * 227s * E. Figuet * 227s ****************************************************************** 227s 227s Parsing options: 227s Parsing file AlnOptimAuto.bpp for options. 227s Alphabet type .........................: Proteic 227s Sequence file .........................: PF01049_full.txt 227s Sequence format .......................: FASTA file 227s Minimum amount of data per site........: 0.7 227s Filter gap characters..................: yes 227s Filter unresolved characters...........: yes 227s Number of reference sequences..........: 0 227s Total number of sequences..............: 1652 227s Total number of sites..................: 656 227s Compressing sequences..................: 227s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 227s Memory required to store distances (Mb): 20 227s Computing pairwise overlap matrix......: 229s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 229s Clustering linkage mode................: complete 229s Computing cluster tree.................: 234s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 234s Comparison criterion:..................: MaxSites 234s Number of sequences in alignment.......: 1652 234s Number of sites in alignment...........: 129 234s Number of chars in alignment...........: 182603 234s Mean site entropy in alignment.........: 0.394104 234s Choice Node #seq %seq #sites %sites #chars %chars 234s 1) 3294 1647 -5 131 +2 184716 2113 235s Number of sequences in alignment.......: 1647 235s Number of sites in alignment...........: 131 235s Number of chars in alignment...........: 184716 235s Mean site entropy in alignment.........: 0.394659 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3286 1645 -2 132 +1 185817 1101 235s Number of sequences in alignment.......: 1645 235s Number of sites in alignment...........: 132 235s Number of chars in alignment...........: 185817 235s Mean site entropy in alignment.........: 0.394872 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 536 1644 -1 133 +1 186943 1126 235s Number of sequences in alignment.......: 1644 235s Number of sites in alignment...........: 133 235s Number of chars in alignment...........: 186943 235s Mean site entropy in alignment.........: 0.39494 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3270 1634 -10 134 +1 187657 714 235s Number of sequences in alignment.......: 1634 235s Number of sites in alignment...........: 134 235s Number of chars in alignment...........: 187657 235s Mean site entropy in alignment.........: 0.395564 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 2951 1627 -7 135 +1 188449 792 235s Number of sequences in alignment.......: 1627 235s Number of sites in alignment...........: 135 235s Number of chars in alignment...........: 188449 235s Mean site entropy in alignment.........: 0.392385 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3021 1614 -13 136 +1 188658 209 235s Number of sequences in alignment.......: 1614 235s Number of sites in alignment...........: 136 235s Number of chars in alignment...........: 188658 235s Mean site entropy in alignment.........: 0.391197 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3235 1545 -69 137 +1 185332 -3326 235s Number of sequences in alignment.......: 1545 235s Number of sites in alignment...........: 137 235s Number of chars in alignment...........: 185332 235s Mean site entropy in alignment.........: 0.389695 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3249 1542 -3 138 +1 186300 968 235s Number of sequences in alignment.......: 1542 235s Number of sites in alignment...........: 138 235s Number of chars in alignment...........: 186300 235s Mean site entropy in alignment.........: 0.389735 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3247 1537 -5 139 +1 187136 836 235s Number of sequences in alignment.......: 1537 235s Number of sites in alignment...........: 139 235s Number of chars in alignment...........: 187136 235s Mean site entropy in alignment.........: 0.389763 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 2816 1521 -16 140 +1 186509 -627 235s Number of sequences in alignment.......: 1521 235s Number of sites in alignment...........: 140 235s Number of chars in alignment...........: 186509 235s Mean site entropy in alignment.........: 0.38832 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3130 1471 -50 141 +1 183898 -2611 235s Number of sequences in alignment.......: 1471 235s Number of sites in alignment...........: 141 235s Number of chars in alignment...........: 183898 235s Mean site entropy in alignment.........: 0.370103 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 1147 1470 -1 142 +1 184902 1004 235s Number of sequences in alignment.......: 1470 235s Number of sites in alignment...........: 142 235s Number of chars in alignment...........: 184902 235s Mean site entropy in alignment.........: 0.370154 235s Choice Node #seq %seq #sites %sites #chars %chars 235s 1) 3251 1465 -5 143 +1 185674 772 236s Number of sequences in alignment.......: 1465 236s Number of sites in alignment...........: 143 236s Number of chars in alignment...........: 185674 236s Mean site entropy in alignment.........: 0.370155 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3280 1391 -74 144 +1 181655 -4019 236s Number of sequences in alignment.......: 1391 236s Number of sites in alignment...........: 144 236s Number of chars in alignment...........: 181655 236s Mean site entropy in alignment.........: 0.359169 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2928 1340 -51 145 +1 177148 -4507 236s Number of sequences in alignment.......: 1340 236s Number of sites in alignment...........: 145 236s Number of chars in alignment...........: 177148 236s Mean site entropy in alignment.........: 0.351822 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 3168 1159 -181 146 +1 163916 -13232 236s Number of sequences in alignment.......: 1159 236s Number of sites in alignment...........: 146 236s Number of chars in alignment...........: 163916 236s Mean site entropy in alignment.........: 0.32945 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2651 1117 -42 147 +1 158726 -5190 236s Number of sequences in alignment.......: 1117 236s Number of sites in alignment...........: 147 236s Number of chars in alignment...........: 158726 236s Mean site entropy in alignment.........: 0.331341 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2242 1097 -20 148 +1 156673 -2053 236s Number of sequences in alignment.......: 1097 236s Number of sites in alignment...........: 148 236s Number of chars in alignment...........: 156673 236s Mean site entropy in alignment.........: 0.324708 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2221 1078 -19 149 +1 154673 -2000 236s Number of sequences in alignment.......: 1078 236s Number of sites in alignment...........: 149 236s Number of chars in alignment...........: 154673 236s Mean site entropy in alignment.........: 0.326137 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2944 993 -85 150 +1 144901 -9772 236s Number of sequences in alignment.......: 993 236s Number of sites in alignment...........: 150 236s Number of chars in alignment...........: 144901 236s Mean site entropy in alignment.........: 0.302006 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2554 941 -52 151 +1 137854 -7047 236s Number of sequences in alignment.......: 941 236s Number of sites in alignment...........: 151 236s Number of chars in alignment...........: 137854 236s Mean site entropy in alignment.........: 0.304205 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2675 234 -707 157 +6 36220 -101634 236s Number of sequences in alignment.......: 234 236s Number of sites in alignment...........: 157 236s Number of chars in alignment...........: 36220 236s Mean site entropy in alignment.........: 0.18992 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 2046 230 -4 158 +1 35777 -443 236s Number of sequences in alignment.......: 230 236s Number of sites in alignment...........: 158 236s Number of chars in alignment...........: 35777 236s Mean site entropy in alignment.........: 0.188188 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1950 24 -206 160 +2 3795 -31982 236s Number of sequences in alignment.......: 24 236s Number of sites in alignment...........: 160 236s Number of chars in alignment...........: 3795 236s Mean site entropy in alignment.........: 0.185344 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1896 20 -4 161 +1 3193 -602 236s Number of sequences in alignment.......: 20 236s Number of sites in alignment...........: 161 236s Number of chars in alignment...........: 3193 236s Mean site entropy in alignment.........: 0.133241 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1795 18 -2 163 +2 2911 -282 236s Number of sequences in alignment.......: 18 236s Number of sites in alignment...........: 163 236s Number of chars in alignment...........: 2911 236s Mean site entropy in alignment.........: 0.122561 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1718 14 -4 165 +2 2294 -617 236s Number of sequences in alignment.......: 14 236s Number of sites in alignment...........: 165 236s Number of chars in alignment...........: 2294 236s Mean site entropy in alignment.........: 0.0452968 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1707 12 -2 166 +1 1983 -311 236s Number of sequences in alignment.......: 12 236s Number of sites in alignment...........: 166 236s Number of chars in alignment...........: 1983 236s Mean site entropy in alignment.........: 0.0379699 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 397 11 -1 168 +2 1838 -145 236s Number of sequences in alignment.......: 11 236s Number of sites in alignment...........: 168 236s Number of chars in alignment...........: 1838 236s Mean site entropy in alignment.........: 0.03305 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1682 8 -3 169 +1 1349 -489 236s Number of sequences in alignment.......: 8 236s Number of sites in alignment...........: 169 236s Number of chars in alignment...........: 1349 236s Mean site entropy in alignment.........: 0.0183685 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 46 7 -1 172 +3 1196 -153 236s Number of sequences in alignment.......: 7 236s Number of sites in alignment...........: 172 236s Number of chars in alignment...........: 1196 236s Mean site entropy in alignment.........: 0.0178367 236s Choice Node #seq %seq #sites %sites #chars %chars 236s 1) 1664 2 -5 176 +4 352 -844 236s Number of sequences in alignment.......: 2 236s Number of sites in alignment...........: 176 236s Number of chars in alignment...........: 352 236s Mean site entropy in alignment.........: 0.010038 236s Choice Node #seq %seq #sites %sites #chars %chars 236s BppAlnOpt's done. Bye. 236s Total execution time: 0.000000d, 0.000000h, 0.000000m, 9.000000s. 236s ****************************************************************** 236s * Bio++ Alignment Optimizer, version 1.1.0. * 236s * Author: J. Dutheil Last Modif. 14/03/18 * 236s * E. Figuet * 236s ****************************************************************** 236s 236s Parsing options: 236s Parsing file AlnOptimAuto.bpp for options. 236s Alphabet type .........................: Proteic 236s Sequence file .........................: PF01049_full.txt 236s Sequence format .......................: FASTA file 236s Minimum amount of data per site........: 0.7 236s Filter gap characters..................: yes 236s Filter unresolved characters...........: yes 236s Number of reference sequences..........: 0 236s Total number of sequences..............: 1652 236s Total number of sites..................: 656 236s Compressing sequences..................: 236s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 236s Memory required to store distances (Mb): 20 236s Computing pairwise overlap matrix......: 238s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 238s Clustering linkage mode................: single 238s Computing cluster tree.................: 244s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 244s Comparison criterion:..................: MaxSites 244s Number of sequences in alignment.......: 1652 244s Number of sites in alignment...........: 129 244s Number of chars in alignment...........: 182603 244s Mean site entropy in alignment.........: 0.394104 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3297 1647 -5 131 +2 184776 2173 244s Number of sequences in alignment.......: 1647 244s Number of sites in alignment...........: 131 244s Number of chars in alignment...........: 184776 244s Mean site entropy in alignment.........: 0.394536 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3295 1645 -2 132 +1 185874 1098 244s Number of sequences in alignment.......: 1645 244s Number of sites in alignment...........: 132 244s Number of chars in alignment...........: 185874 244s Mean site entropy in alignment.........: 0.394721 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 181 1644 -1 133 +1 186998 1124 244s Number of sequences in alignment.......: 1644 244s Number of sites in alignment...........: 133 244s Number of chars in alignment...........: 186998 244s Mean site entropy in alignment.........: 0.394677 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3285 1634 -10 134 +1 187772 774 245s Number of sequences in alignment.......: 1634 245s Number of sites in alignment...........: 134 245s Number of chars in alignment...........: 187772 245s Mean site entropy in alignment.........: 0.395614 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 3278 1627 -7 135 +1 188620 848 245s Number of sequences in alignment.......: 1627 245s Number of sites in alignment...........: 135 245s Number of chars in alignment...........: 188620 245s Mean site entropy in alignment.........: 0.396053 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 3265 1614 -13 136 +1 189192 572 245s Number of sequences in alignment.......: 1614 245s Number of sites in alignment...........: 136 245s Number of chars in alignment...........: 189192 245s Mean site entropy in alignment.........: 0.396866 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 3157 1505 -109 137 +1 184306 -4886 245s Number of sequences in alignment.......: 1505 245s Number of sites in alignment...........: 137 245s Number of chars in alignment...........: 184306 245s Mean site entropy in alignment.........: 0.397698 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 3139 1488 -17 138 +1 184277 -29 245s Number of sequences in alignment.......: 1488 245s Number of sites in alignment...........: 138 245s Number of chars in alignment...........: 184277 245s Mean site entropy in alignment.........: 0.396924 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 3136 1485 -3 139 +1 185134 857 246s Number of sequences in alignment.......: 1485 246s Number of sites in alignment...........: 139 246s Number of chars in alignment...........: 185134 246s Mean site entropy in alignment.........: 0.396707 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 3122 1471 -14 140 +1 185214 80 246s Number of sequences in alignment.......: 1471 246s Number of sites in alignment...........: 140 246s Number of chars in alignment...........: 185214 246s Mean site entropy in alignment.........: 0.396624 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 2848 1437 -34 141 +1 183753 -1461 246s Number of sequences in alignment.......: 1437 246s Number of sites in alignment...........: 141 246s Number of chars in alignment...........: 183753 246s Mean site entropy in alignment.........: 0.379676 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 3110 1425 -12 142 +1 183898 145 246s Number of sequences in alignment.......: 1425 246s Number of sites in alignment...........: 142 246s Number of chars in alignment...........: 183898 246s Mean site entropy in alignment.........: 0.379975 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 3073 1387 -38 143 +1 182369 -1529 246s Number of sequences in alignment.......: 1387 246s Number of sites in alignment...........: 143 246s Number of chars in alignment...........: 182369 246s Mean site entropy in alignment.........: 0.376594 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 2904 1380 -7 144 +1 182593 224 246s Number of sequences in alignment.......: 1380 246s Number of sites in alignment...........: 144 246s Number of chars in alignment...........: 182593 246s Mean site entropy in alignment.........: 0.375989 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 2941 1206 -174 145 +1 167869 -14724 246s Number of sequences in alignment.......: 1206 246s Number of sites in alignment...........: 145 246s Number of chars in alignment...........: 167869 246s Mean site entropy in alignment.........: 0.346494 246s Choice Node #seq %seq #sites %sites #chars %chars 246s 1) 2829 1145 -61 146 +1 162413 -5456 247s Number of sequences in alignment.......: 1145 247s Number of sites in alignment...........: 146 247s Number of chars in alignment...........: 162413 247s Mean site entropy in alignment.........: 0.332586 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2751 1071 -74 147 +1 153723 -8690 247s Number of sequences in alignment.......: 1071 247s Number of sites in alignment...........: 147 247s Number of chars in alignment...........: 153723 247s Mean site entropy in alignment.........: 0.320762 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1751 998 -73 148 +1 144121 -9602 247s Number of sequences in alignment.......: 998 247s Number of sites in alignment...........: 148 247s Number of chars in alignment...........: 144121 247s Mean site entropy in alignment.........: 0.298818 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2100 985 -13 149 +1 142964 -1157 247s Number of sequences in alignment.......: 985 247s Number of sites in alignment...........: 149 247s Number of chars in alignment...........: 142964 247s Mean site entropy in alignment.........: 0.298279 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2427 665 -320 150 +1 97526 -45438 247s Number of sequences in alignment.......: 665 247s Number of sites in alignment...........: 150 247s Number of chars in alignment...........: 97526 247s Mean site entropy in alignment.........: 0.293825 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1379 664 -1 151 +1 97882 356 247s Number of sequences in alignment.......: 664 247s Number of sites in alignment...........: 151 247s Number of chars in alignment...........: 97882 247s Mean site entropy in alignment.........: 0.292162 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2203 441 -223 152 +1 65487 -32395 247s Number of sequences in alignment.......: 441 247s Number of sites in alignment...........: 152 247s Number of chars in alignment...........: 65487 247s Mean site entropy in alignment.........: 0.29729 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2189 427 -14 153 +1 63726 -1761 247s Number of sequences in alignment.......: 427 247s Number of sites in alignment...........: 153 247s Number of chars in alignment...........: 63726 247s Mean site entropy in alignment.........: 0.295662 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2082 334 -93 154 +1 50320 -13406 247s Number of sequences in alignment.......: 334 247s Number of sites in alignment...........: 154 247s Number of chars in alignment...........: 50320 247s Mean site entropy in alignment.........: 0.268583 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 2006 258 -76 155 +1 39190 -11130 247s Number of sequences in alignment.......: 258 247s Number of sites in alignment...........: 155 247s Number of chars in alignment...........: 39190 247s Mean site entropy in alignment.........: 0.230649 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1987 254 -4 156 +1 38780 -410 247s Number of sequences in alignment.......: 254 247s Number of sites in alignment...........: 156 247s Number of chars in alignment...........: 38780 247s Mean site entropy in alignment.........: 0.228398 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1915 247 -7 157 +1 37896 -884 247s Number of sequences in alignment.......: 247 247s Number of sites in alignment...........: 157 247s Number of chars in alignment...........: 37896 247s Mean site entropy in alignment.........: 0.226904 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1876 130 -117 158 +1 20276 -17620 247s Number of sequences in alignment.......: 130 247s Number of sites in alignment...........: 158 247s Number of chars in alignment...........: 20276 247s Mean site entropy in alignment.........: 0.134572 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1704 3 -127 163 +5 489 -19787 247s Number of sequences in alignment.......: 3 247s Number of sites in alignment...........: 163 247s Number of chars in alignment...........: 489 247s Mean site entropy in alignment.........: 0.065727 247s Choice Node #seq %seq #sites %sites #chars %chars 247s 1) 1474 2 -1 167 +4 334 -155 247s Number of sequences in alignment.......: 2 247s Number of sites in alignment...........: 167 247s Number of chars in alignment...........: 334 247s Mean site entropy in alignment.........: 0.0338121 247s Choice Node #seq %seq #sites %sites #chars %chars 247s BppAlnOpt's done. Bye. 247s Total execution time: 0.000000d, 0.000000h, 0.000000m, 11.000000s. 247s ****************************************************************** 247s * Bio++ Alignment Optimizer, version 1.1.0. * 247s * Author: J. Dutheil Last Modif. 14/03/18 * 247s * E. Figuet * 247s ****************************************************************** 247s 247s Parsing options: 247s Parsing file AlnOptimAuto.bpp for options. 247s Alphabet type .........................: Proteic 247s Sequence file .........................: PF01049_full.txt 247s Sequence format .......................: FASTA file 247s Minimum amount of data per site........: 0.7 247s Filter gap characters..................: yes 247s Filter unresolved characters...........: yes 247s Number of reference sequences..........: 0 247s Total number of sequences..............: 1652 247s Total number of sites..................: 656 247s Compressing sequences..................: 247s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 247s Memory required to store distances (Mb): 20 247s Computing pairwise overlap matrix......: 249s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 249s Clustering linkage mode................: average 249s Computing cluster tree.................: 255s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 255s Comparison criterion:..................: MaxSites 255s Number of sequences in alignment.......: 1652 255s Number of sites in alignment...........: 129 255s Number of chars in alignment...........: 182603 255s Mean site entropy in alignment.........: 0.394104 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3299 1647 -5 131 +2 184774 2171 255s Number of sequences in alignment.......: 1647 255s Number of sites in alignment...........: 131 255s Number of chars in alignment...........: 184774 255s Mean site entropy in alignment.........: 0.394431 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3293 1645 -2 132 +1 185875 1101 255s Number of sequences in alignment.......: 1645 255s Number of sites in alignment...........: 132 255s Number of chars in alignment...........: 185875 255s Mean site entropy in alignment.........: 0.394643 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 181 1644 -1 133 +1 186999 1124 255s Number of sequences in alignment.......: 1644 255s Number of sites in alignment...........: 133 255s Number of chars in alignment...........: 186999 255s Mean site entropy in alignment.........: 0.394599 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3287 1634 -10 134 +1 187779 780 255s Number of sequences in alignment.......: 1634 255s Number of sites in alignment...........: 134 255s Number of chars in alignment...........: 187779 255s Mean site entropy in alignment.........: 0.395631 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3276 1627 -7 135 +1 188617 838 255s Number of sequences in alignment.......: 1627 255s Number of sites in alignment...........: 135 255s Number of chars in alignment...........: 188617 255s Mean site entropy in alignment.........: 0.396076 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3238 1614 -13 136 +1 189013 396 255s Number of sequences in alignment.......: 1614 255s Number of sites in alignment...........: 136 255s Number of chars in alignment...........: 189013 255s Mean site entropy in alignment.........: 0.395128 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3023 1533 -81 138 +2 185240 -3773 255s Number of sequences in alignment.......: 1533 255s Number of sites in alignment...........: 138 255s Number of chars in alignment...........: 185240 255s Mean site entropy in alignment.........: 0.372196 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 516 1532 -1 139 +1 186276 1036 256s Number of sequences in alignment.......: 1532 256s Number of sites in alignment...........: 139 256s Number of chars in alignment...........: 186276 256s Mean site entropy in alignment.........: 0.372193 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3282 1521 -11 140 +1 186867 591 256s Number of sequences in alignment.......: 1521 256s Number of sites in alignment...........: 140 256s Number of chars in alignment...........: 186867 256s Mean site entropy in alignment.........: 0.372497 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3105 1482 -39 141 +1 185210 -1657 256s Number of sequences in alignment.......: 1482 256s Number of sites in alignment...........: 141 256s Number of chars in alignment...........: 185210 256s Mean site entropy in alignment.........: 0.368185 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3135 1471 -11 142 +1 185562 352 256s Number of sequences in alignment.......: 1471 256s Number of sites in alignment...........: 142 256s Number of chars in alignment...........: 185562 256s Mean site entropy in alignment.........: 0.367384 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2863 1455 -16 143 +1 184869 -693 256s Number of sequences in alignment.......: 1455 256s Number of sites in alignment...........: 143 256s Number of chars in alignment...........: 184869 256s Mean site entropy in alignment.........: 0.366056 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3166 1413 -42 144 +1 183102 -1767 256s Number of sequences in alignment.......: 1413 256s Number of sites in alignment...........: 144 256s Number of chars in alignment...........: 183102 256s Mean site entropy in alignment.........: 0.362023 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2996 1204 -209 145 +1 168239 -14863 256s Number of sequences in alignment.......: 1204 256s Number of sites in alignment...........: 145 256s Number of chars in alignment...........: 168239 256s Mean site entropy in alignment.........: 0.339856 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2960 1154 -50 146 +1 163602 -4637 256s Number of sequences in alignment.......: 1154 256s Number of sites in alignment...........: 146 256s Number of chars in alignment...........: 163602 256s Mean site entropy in alignment.........: 0.330406 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2808 1094 -60 147 +1 157058 -6544 256s Number of sequences in alignment.......: 1094 256s Number of sites in alignment...........: 147 256s Number of chars in alignment...........: 157058 256s Mean site entropy in alignment.........: 0.314388 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2635 1059 -35 148 +1 152818 -4240 256s Number of sequences in alignment.......: 1059 256s Number of sites in alignment...........: 148 256s Number of chars in alignment...........: 152818 256s Mean site entropy in alignment.........: 0.315749 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 1934 1048 -11 149 +1 152007 -811 256s Number of sequences in alignment.......: 1048 256s Number of sites in alignment...........: 149 256s Number of chars in alignment...........: 152007 256s Mean site entropy in alignment.........: 0.310007 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 1961 1030 -18 150 +1 150229 -1778 256s Number of sequences in alignment.......: 1030 256s Number of sites in alignment...........: 150 256s Number of chars in alignment...........: 150229 256s Mean site entropy in alignment.........: 0.303664 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2640 451 -579 151 +1 67067 -83162 256s Number of sequences in alignment.......: 451 256s Number of sites in alignment...........: 151 256s Number of chars in alignment...........: 67067 256s Mean site entropy in alignment.........: 0.278258 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2434 425 -26 152 +1 63569 -3498 256s Number of sequences in alignment.......: 425 256s Number of sites in alignment...........: 152 256s Number of chars in alignment...........: 63569 256s Mean site entropy in alignment.........: 0.276822 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2332 391 -34 153 +1 58841 -4728 256s Number of sequences in alignment.......: 391 256s Number of sites in alignment...........: 153 256s Number of chars in alignment...........: 58841 256s Mean site entropy in alignment.........: 0.269678 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2039 342 -49 154 +1 51693 -7148 256s Number of sequences in alignment.......: 342 256s Number of sites in alignment...........: 154 256s Number of chars in alignment...........: 51693 256s Mean site entropy in alignment.........: 0.250803 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2337 280 -62 155 +1 42698 -8995 256s Number of sequences in alignment.......: 280 256s Number of sites in alignment...........: 155 256s Number of chars in alignment...........: 42698 256s Mean site entropy in alignment.........: 0.230831 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 1969 277 -3 156 +1 42454 -244 256s Number of sequences in alignment.......: 277 256s Number of sites in alignment...........: 156 256s Number of chars in alignment...........: 42454 256s Mean site entropy in alignment.........: 0.228862 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 2097 246 -31 157 +1 37949 -4505 256s Number of sequences in alignment.......: 246 256s Number of sites in alignment...........: 157 256s Number of chars in alignment...........: 37949 256s Mean site entropy in alignment.........: 0.216654 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 884 245 -1 158 +1 37976 27 257s Number of sequences in alignment.......: 245 257s Number of sites in alignment...........: 158 257s Number of chars in alignment...........: 37976 257s Mean site entropy in alignment.........: 0.215946 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 1937 19 -226 163 +5 3067 -34909 257s Number of sequences in alignment.......: 19 257s Number of sites in alignment...........: 163 257s Number of chars in alignment...........: 3067 257s Mean site entropy in alignment.........: 0.115126 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 1719 14 -5 165 +2 2297 -770 257s Number of sequences in alignment.......: 14 257s Number of sites in alignment...........: 165 257s Number of chars in alignment...........: 2297 257s Mean site entropy in alignment.........: 0.0991142 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 1699 12 -2 166 +1 1983 -314 257s Number of sequences in alignment.......: 12 257s Number of sites in alignment...........: 166 257s Number of chars in alignment...........: 1983 257s Mean site entropy in alignment.........: 0.0379699 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 397 11 -1 168 +2 1838 -145 257s Number of sequences in alignment.......: 11 257s Number of sites in alignment...........: 168 257s Number of chars in alignment...........: 1838 257s Mean site entropy in alignment.........: 0.03305 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 1684 8 -3 169 +1 1349 -489 257s Number of sequences in alignment.......: 8 257s Number of sites in alignment...........: 169 257s Number of chars in alignment...........: 1349 257s Mean site entropy in alignment.........: 0.0183685 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 46 7 -1 172 +3 1196 -153 257s Number of sequences in alignment.......: 7 257s Number of sites in alignment...........: 172 257s Number of chars in alignment...........: 1196 257s Mean site entropy in alignment.........: 0.0178367 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 1664 2 -5 176 +4 352 -844 257s Number of sequences in alignment.......: 2 257s Number of sites in alignment...........: 176 257s Number of chars in alignment...........: 352 257s Mean site entropy in alignment.........: 0.010038 257s Choice Node #seq %seq #sites %sites #chars %chars 257s BppAlnOpt's done. Bye. 257s Total execution time: 0.000000d, 0.000000h, 0.000000m, 9.000000s. 257s ****************************************************************** 257s * Bio++ Alignment Optimizer, version 1.1.0. * 257s * Author: J. Dutheil Last Modif. 14/03/18 * 257s * E. Figuet * 257s ****************************************************************** 257s 257s Parsing options: 257s Parsing file AlnOptimAuto.bpp for options. 257s Alphabet type .........................: Proteic 257s Sequence file .........................: PF01049_full.txt 257s Sequence format .......................: FASTA file 257s Minimum amount of data per site........: 0.7 257s Filter gap characters..................: yes 257s Filter unresolved characters...........: yes 257s Number of reference sequences..........: 0 257s Total number of sequences..............: 1652 257s Total number of sites..................: 656 257s Compressing sequences..................: 257s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 257s Memory required to store distances (Mb): 20 257s Computing pairwise overlap matrix......: 259s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 259s Clustering linkage mode................: median 259s Computing cluster tree.................: 264s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 264s Comparison criterion:..................: MaxSites 264s Number of sequences in alignment.......: 1652 264s Number of sites in alignment...........: 129 264s Number of chars in alignment...........: 182603 264s Mean site entropy in alignment.........: 0.394104 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 3297 1647 -5 131 +2 184774 2171 264s Number of sequences in alignment.......: 1647 264s Number of sites in alignment...........: 131 264s Number of chars in alignment...........: 184774 264s Mean site entropy in alignment.........: 0.394431 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 3295 1645 -2 132 +1 185873 1099 264s Number of sequences in alignment.......: 1645 264s Number of sites in alignment...........: 132 264s Number of chars in alignment...........: 185873 264s Mean site entropy in alignment.........: 0.394618 264s Choice Node #seq %seq #sites %sites #chars %chars 264s 1) 275 1644 -1 133 +1 186998 1125 265s Number of sequences in alignment.......: 1644 265s Number of sites in alignment...........: 133 265s Number of chars in alignment...........: 186998 265s Mean site entropy in alignment.........: 0.394724 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 3280 1630 -14 134 +1 187559 561 265s Number of sequences in alignment.......: 1630 265s Number of sites in alignment...........: 134 265s Number of chars in alignment...........: 187559 265s Mean site entropy in alignment.........: 0.39546 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 3272 1622 -8 135 +1 188376 817 265s Number of sequences in alignment.......: 1622 265s Number of sites in alignment...........: 135 265s Number of chars in alignment...........: 188376 265s Mean site entropy in alignment.........: 0.396213 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 3261 1611 -11 136 +1 189031 655 265s Number of sequences in alignment.......: 1611 265s Number of sites in alignment...........: 136 265s Number of chars in alignment...........: 189031 265s Mean site entropy in alignment.........: 0.396902 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 3184 1534 -77 137 +1 185562 -3469 265s Number of sequences in alignment.......: 1534 265s Number of sites in alignment...........: 137 265s Number of chars in alignment...........: 185562 265s Mean site entropy in alignment.........: 0.396433 265s Choice Node #seq %seq #sites %sites #chars %chars 265s 1) 3182 1532 -2 138 +1 186503 941 266s Number of sequences in alignment.......: 1532 266s Number of sites in alignment...........: 138 266s Number of chars in alignment...........: 186503 266s Mean site entropy in alignment.........: 0.396422 266s Choice Node #seq %seq #sites %sites #chars %chars 266s 1) 513 1531 -1 139 +1 187535 1032 266s Number of sequences in alignment.......: 1531 266s Number of sites in alignment...........: 139 266s Number of chars in alignment...........: 187535 266s Mean site entropy in alignment.........: 0.396222 266s Choice Node #seq %seq #sites %sites #chars %chars 266s 1) 3169 1518 -13 140 +1 187760 225 266s Number of sequences in alignment.......: 1518 266s Number of sites in alignment...........: 140 266s Number of chars in alignment...........: 187760 266s Mean site entropy in alignment.........: 0.395785 266s Choice Node #seq %seq #sites %sites #chars %chars 266s 1) 3125 1475 -43 141 +1 185962 -1798 266s Number of sequences in alignment.......: 1475 266s Number of sites in alignment...........: 141 266s Number of chars in alignment...........: 185962 266s Mean site entropy in alignment.........: 0.388512 266s Choice Node #seq %seq #sites %sites #chars %chars 266s 1) 3117 1467 -8 142 +1 186502 540 266s Number of sequences in alignment.......: 1467 266s Number of sites in alignment...........: 142 266s Number of chars in alignment...........: 186502 266s Mean site entropy in alignment.........: 0.388016 266s Choice Node #seq %seq #sites %sites #chars %chars 266s 1) 3102 1452 -15 143 +1 186490 -12 267s Number of sequences in alignment.......: 1452 267s Number of sites in alignment...........: 143 267s Number of chars in alignment...........: 186490 267s Mean site entropy in alignment.........: 0.386609 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 3052 1402 -50 144 +1 183727 -2763 267s Number of sequences in alignment.......: 1402 267s Number of sites in alignment...........: 144 267s Number of chars in alignment...........: 183727 267s Mean site entropy in alignment.........: 0.379315 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2877 1227 -175 145 +1 170235 -13492 267s Number of sequences in alignment.......: 1227 267s Number of sites in alignment...........: 145 267s Number of chars in alignment...........: 170235 267s Mean site entropy in alignment.........: 0.34859 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2788 1138 -89 146 +1 161621 -8614 267s Number of sequences in alignment.......: 1138 267s Number of sites in alignment...........: 146 267s Number of chars in alignment...........: 161621 267s Mean site entropy in alignment.........: 0.330459 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2731 1081 -57 147 +1 155136 -6485 267s Number of sequences in alignment.......: 1081 267s Number of sites in alignment...........: 147 267s Number of chars in alignment...........: 155136 267s Mean site entropy in alignment.........: 0.319787 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 1701 1030 -51 148 +1 148555 -6581 267s Number of sequences in alignment.......: 1030 267s Number of sites in alignment...........: 148 267s Number of chars in alignment...........: 148555 267s Mean site entropy in alignment.........: 0.305707 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2499 798 -232 149 +1 116805 -31750 267s Number of sequences in alignment.......: 798 267s Number of sites in alignment...........: 149 267s Number of chars in alignment...........: 116805 267s Mean site entropy in alignment.........: 0.273968 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2468 767 -31 150 +1 112894 -3911 267s Number of sequences in alignment.......: 767 267s Number of sites in alignment...........: 150 267s Number of chars in alignment...........: 112894 267s Mean site entropy in alignment.........: 0.272075 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2239 538 -229 151 +1 79674 -33220 267s Number of sequences in alignment.......: 538 267s Number of sites in alignment...........: 151 267s Number of chars in alignment...........: 79674 267s Mean site entropy in alignment.........: 0.280963 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2196 495 -43 152 +1 73702 -5972 267s Number of sequences in alignment.......: 495 267s Number of sites in alignment...........: 152 267s Number of chars in alignment...........: 73702 267s Mean site entropy in alignment.........: 0.28148 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2076 375 -120 153 +1 56316 -17386 267s Number of sequences in alignment.......: 375 267s Number of sites in alignment...........: 153 267s Number of chars in alignment...........: 56316 267s Mean site entropy in alignment.........: 0.267502 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 2018 317 -58 154 +1 47977 -8339 267s Number of sequences in alignment.......: 317 267s Number of sites in alignment...........: 154 267s Number of chars in alignment...........: 47977 267s Mean site entropy in alignment.........: 0.249671 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 1949 248 -69 155 +1 37817 -10160 267s Number of sequences in alignment.......: 248 267s Number of sites in alignment...........: 155 267s Number of chars in alignment...........: 37817 267s Mean site entropy in alignment.........: 0.215239 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 1938 237 -11 156 +1 36376 -1441 267s Number of sequences in alignment.......: 237 267s Number of sites in alignment...........: 156 267s Number of chars in alignment...........: 36376 267s Mean site entropy in alignment.........: 0.201826 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 1926 225 -12 157 +1 34752 -1624 267s Number of sequences in alignment.......: 225 267s Number of sites in alignment...........: 157 267s Number of chars in alignment...........: 34752 267s Mean site entropy in alignment.........: 0.184033 267s Choice Node #seq %seq #sites %sites #chars %chars 267s 1) 1779 78 -147 158 +1 12282 -22470 268s Number of sequences in alignment.......: 78 268s Number of sites in alignment...........: 158 268s Number of chars in alignment...........: 12282 268s Mean site entropy in alignment.........: 0.0830049 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1703 2 -76 160 +2 320 -11962 268s Number of sequences in alignment.......: 2 268s Number of sites in alignment...........: 160 268s Number of chars in alignment...........: 320 268s Mean site entropy in alignment.........: 0 268s Choice Node #seq %seq #sites %sites #chars %chars 268s BppAlnOpt's done. Bye. 268s Total execution time: 0.000000d, 0.000000h, 0.000000m, 10.000000s. 268s ****************************************************************** 268s * Bio++ Alignment Optimizer, version 1.1.0. * 268s * Author: J. Dutheil Last Modif. 14/03/18 * 268s * E. Figuet * 268s ****************************************************************** 268s 268s Parsing options: 268s Parsing file AlnOptimAuto.bpp for options. 268s Alphabet type .........................: Proteic 268s Sequence file .........................: PF01049_full.txt 268s Sequence format .......................: FASTA file 268s Minimum amount of data per site........: 0.7 268s Filter gap characters..................: yes 268s Filter unresolved characters...........: yes 268s Number of reference sequences..........: 0 268s Total number of sequences..............: 1652 268s Total number of sites..................: 656 268s Compressing sequences..................: 268s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 268s Memory required to store distances (Mb): 20 268s Computing pairwise overlap matrix......: 270s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 270s Clustering linkage mode................: centroid 270s Computing cluster tree.................: 275s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 275s Comparison criterion:..................: MaxSites 275s Number of sequences in alignment.......: 1652 275s Number of sites in alignment...........: 129 275s Number of chars in alignment...........: 182603 275s Mean site entropy in alignment.........: 0.394104 275s Choice Node #seq %seq #sites %sites #chars %chars 275s 1) 3297 1647 -5 131 +2 184783 2180 276s Number of sequences in alignment.......: 1647 276s Number of sites in alignment...........: 131 276s Number of chars in alignment...........: 184783 276s Mean site entropy in alignment.........: 0.394537 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3295 1645 -2 132 +1 185880 1097 276s Number of sequences in alignment.......: 1645 276s Number of sites in alignment...........: 132 276s Number of chars in alignment...........: 185880 276s Mean site entropy in alignment.........: 0.394662 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 181 1644 -1 133 +1 187004 1124 276s Number of sequences in alignment.......: 1644 276s Number of sites in alignment...........: 133 276s Number of chars in alignment...........: 187004 276s Mean site entropy in alignment.........: 0.394618 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3284 1634 -10 134 +1 187785 781 276s Number of sequences in alignment.......: 1634 276s Number of sites in alignment...........: 134 276s Number of chars in alignment...........: 187785 276s Mean site entropy in alignment.........: 0.395449 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3277 1627 -7 135 +1 188649 864 276s Number of sequences in alignment.......: 1627 276s Number of sites in alignment...........: 135 276s Number of chars in alignment...........: 188649 276s Mean site entropy in alignment.........: 0.395884 276s Choice Node #seq %seq #sites %sites #chars %chars 276s 1) 3264 1614 -13 136 +1 189270 621 277s Number of sequences in alignment.......: 1614 277s Number of sites in alignment...........: 136 277s Number of chars in alignment...........: 189270 277s Mean site entropy in alignment.........: 0.396209 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3158 1508 -106 137 +1 184807 -4463 277s Number of sequences in alignment.......: 1508 277s Number of sites in alignment...........: 137 277s Number of chars in alignment...........: 184807 277s Mean site entropy in alignment.........: 0.391659 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3141 1491 -17 138 +1 184810 3 277s Number of sequences in alignment.......: 1491 277s Number of sites in alignment...........: 138 277s Number of chars in alignment...........: 184810 277s Mean site entropy in alignment.........: 0.389899 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3135 1485 -6 139 +1 185468 658 277s Number of sequences in alignment.......: 1485 277s Number of sites in alignment...........: 139 277s Number of chars in alignment...........: 185468 277s Mean site entropy in alignment.........: 0.389868 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3124 1474 -11 140 +1 185788 320 277s Number of sequences in alignment.......: 1474 277s Number of sites in alignment...........: 140 277s Number of chars in alignment...........: 185788 277s Mean site entropy in alignment.........: 0.389071 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3091 1441 -33 141 +1 184655 -1133 277s Number of sequences in alignment.......: 1441 277s Number of sites in alignment...........: 141 277s Number of chars in alignment...........: 184655 277s Mean site entropy in alignment.........: 0.38709 277s Choice Node #seq %seq #sites %sites #chars %chars 277s 1) 3077 1427 -14 142 +1 184714 59 278s Number of sequences in alignment.......: 1427 278s Number of sites in alignment...........: 142 278s Number of chars in alignment...........: 184714 278s Mean site entropy in alignment.........: 0.386526 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 3055 1405 -22 144 +2 185186 472 278s Number of sequences in alignment.......: 1405 278s Number of sites in alignment...........: 144 278s Number of chars in alignment...........: 185186 278s Mean site entropy in alignment.........: 0.383626 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2907 1257 -148 145 +1 173927 -11259 278s Number of sequences in alignment.......: 1257 278s Number of sites in alignment...........: 145 278s Number of chars in alignment...........: 173927 278s Mean site entropy in alignment.........: 0.350796 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2807 1157 -100 146 +1 163983 -9944 278s Number of sequences in alignment.......: 1157 278s Number of sites in alignment...........: 146 278s Number of chars in alignment...........: 163983 278s Mean site entropy in alignment.........: 0.329626 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2748 1098 -59 147 +1 157592 -6391 278s Number of sequences in alignment.......: 1098 278s Number of sites in alignment...........: 147 278s Number of chars in alignment...........: 157592 278s Mean site entropy in alignment.........: 0.314432 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 1678 1070 -28 148 +1 154399 -3193 278s Number of sequences in alignment.......: 1070 278s Number of sites in alignment...........: 148 278s Number of chars in alignment...........: 154399 278s Mean site entropy in alignment.........: 0.303382 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2620 942 -128 149 +1 137516 -16883 278s Number of sequences in alignment.......: 942 278s Number of sites in alignment...........: 149 278s Number of chars in alignment...........: 137516 278s Mean site entropy in alignment.........: 0.284952 278s Choice Node #seq %seq #sites %sites #chars %chars 278s 1) 2615 937 -5 150 +1 137462 -54 279s Number of sequences in alignment.......: 937 279s Number of sites in alignment...........: 150 279s Number of chars in alignment...........: 137462 279s Mean site entropy in alignment.........: 0.285064 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2320 642 -295 151 +1 95140 -42322 279s Number of sequences in alignment.......: 642 279s Number of sites in alignment...........: 151 279s Number of chars in alignment...........: 95140 279s Mean site entropy in alignment.........: 0.276628 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2179 501 -141 152 +1 74734 -20406 279s Number of sequences in alignment.......: 501 279s Number of sites in alignment...........: 152 279s Number of chars in alignment...........: 74734 279s Mean site entropy in alignment.........: 0.281366 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2108 430 -71 153 +1 64604 -10130 279s Number of sequences in alignment.......: 430 279s Number of sites in alignment...........: 153 279s Number of chars in alignment...........: 64604 279s Mean site entropy in alignment.........: 0.282214 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 2038 360 -70 154 +1 54522 -10082 279s Number of sequences in alignment.......: 360 279s Number of sites in alignment...........: 154 279s Number of chars in alignment...........: 54522 279s Mean site entropy in alignment.........: 0.265356 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1969 291 -69 155 +1 44461 -10061 279s Number of sequences in alignment.......: 291 279s Number of sites in alignment...........: 155 279s Number of chars in alignment...........: 44461 279s Mean site entropy in alignment.........: 0.240018 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1956 278 -13 156 +1 42693 -1768 279s Number of sequences in alignment.......: 278 279s Number of sites in alignment...........: 156 279s Number of chars in alignment...........: 42693 279s Mean site entropy in alignment.........: 0.236678 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1925 247 -31 157 +1 38195 -4498 279s Number of sequences in alignment.......: 247 279s Number of sites in alignment...........: 157 279s Number of chars in alignment...........: 38195 279s Mean site entropy in alignment.........: 0.216008 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 1923 245 -2 158 +1 38065 -130 279s Number of sequences in alignment.......: 245 279s Number of sites in alignment...........: 158 279s Number of chars in alignment...........: 38065 279s Mean site entropy in alignment.........: 0.215165 279s Choice Node #seq %seq #sites %sites #chars %chars 279s 1) 610 1 -244 177 +19 177 -37888 279s Number of sequences in alignment.......: 1 279s Number of sites in alignment...........: 177 279s Number of chars in alignment...........: 177 279s Mean site entropy in alignment.........: 0 279s Choice Node #seq %seq #sites %sites #chars %chars 279s BppAlnOpt's done. Bye. 279s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 279s ****************************************************************** 279s * Bio++ Alignment Optimizer, version 1.1.0. * 279s * Author: J. Dutheil Last Modif. 14/03/18 * 279s * E. Figuet * 279s ****************************************************************** 279s 279s Parsing options: 279s Parsing file AlnOptimAuto.bpp for options. 279s Alphabet type .........................: Proteic 279s Sequence file .........................: PF01049_full.txt 279s Sequence format .......................: FASTA file 279s Minimum amount of data per site........: 0.7 279s Filter gap characters..................: yes 279s Filter unresolved characters...........: yes 279s Number of reference sequences..........: 0 279s Total number of sequences..............: 1652 279s Total number of sites..................: 656 279s Compressing sequences..................: 279s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 279s Memory required to store distances (Mb): 20 279s Computing pairwise overlap matrix......: 281s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 281s Clustering linkage mode................: ward 281s Computing cluster tree.................: 287s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 287s Comparison criterion:..................: MaxSites 287s Number of sequences in alignment.......: 1652 287s Number of sites in alignment...........: 129 287s Number of chars in alignment...........: 182603 287s Mean site entropy in alignment.........: 0.394104 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3251 1647 -5 131 +2 184716 2113 287s Number of sequences in alignment.......: 1647 287s Number of sites in alignment...........: 131 287s Number of chars in alignment...........: 184716 287s Mean site entropy in alignment.........: 0.394659 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3239 1645 -2 132 +1 185817 1101 287s Number of sequences in alignment.......: 1645 287s Number of sites in alignment...........: 132 287s Number of chars in alignment...........: 185817 287s Mean site entropy in alignment.........: 0.394872 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 1147 1644 -1 133 +1 186943 1126 287s Number of sequences in alignment.......: 1644 287s Number of sites in alignment...........: 133 287s Number of chars in alignment...........: 186943 287s Mean site entropy in alignment.........: 0.394935 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3219 1634 -10 134 +1 187657 714 287s Number of sequences in alignment.......: 1634 287s Number of sites in alignment...........: 134 287s Number of chars in alignment...........: 187657 287s Mean site entropy in alignment.........: 0.395559 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3259 1627 -7 135 +1 188588 931 287s Number of sequences in alignment.......: 1627 287s Number of sites in alignment...........: 135 287s Number of chars in alignment...........: 188588 287s Mean site entropy in alignment.........: 0.39614 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3098 1614 -13 136 +1 188375 -213 287s Number of sequences in alignment.......: 1614 287s Number of sites in alignment...........: 136 287s Number of chars in alignment...........: 188375 287s Mean site entropy in alignment.........: 0.394599 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3276 1530 -84 139 +3 185744 -2631 287s Number of sequences in alignment.......: 1530 287s Number of sites in alignment...........: 139 287s Number of chars in alignment...........: 185744 287s Mean site entropy in alignment.........: 0.386989 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3232 1521 -9 140 +1 186359 615 287s Number of sequences in alignment.......: 1521 287s Number of sites in alignment...........: 140 287s Number of chars in alignment...........: 186359 287s Mean site entropy in alignment.........: 0.387231 287s Choice Node #seq %seq #sites %sites #chars %chars 287s 1) 3100 1471 -50 141 +1 182091 -4268 288s Number of sequences in alignment.......: 1471 288s Number of sites in alignment...........: 141 288s Number of chars in alignment...........: 182091 288s Mean site entropy in alignment.........: 0.382183 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3094 1451 -20 142 +1 181641 -450 288s Number of sequences in alignment.......: 1451 288s Number of sites in alignment...........: 142 288s Number of chars in alignment...........: 181641 288s Mean site entropy in alignment.........: 0.377306 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3289 1405 -46 143 +1 179756 -1885 288s Number of sequences in alignment.......: 1405 288s Number of sites in alignment...........: 143 288s Number of chars in alignment...........: 179756 288s Mean site entropy in alignment.........: 0.373661 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3024 1397 -8 144 +1 180270 514 288s Number of sequences in alignment.......: 1397 288s Number of sites in alignment...........: 144 288s Number of chars in alignment...........: 180270 288s Mean site entropy in alignment.........: 0.372275 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3298 1308 -89 145 +1 175625 -4645 288s Number of sequences in alignment.......: 1308 288s Number of sites in alignment...........: 145 288s Number of chars in alignment...........: 175625 288s Mean site entropy in alignment.........: 0.348431 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3290 1161 -147 146 +1 156442 -19183 288s Number of sequences in alignment.......: 1161 288s Number of sites in alignment...........: 146 288s Number of chars in alignment...........: 156442 288s Mean site entropy in alignment.........: 0.328649 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 2555 1150 -11 147 +1 155751 -691 288s Number of sequences in alignment.......: 1150 288s Number of sites in alignment...........: 147 288s Number of chars in alignment...........: 155751 288s Mean site entropy in alignment.........: 0.328421 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 2516 1111 -39 148 +1 150876 -4875 288s Number of sequences in alignment.......: 1111 288s Number of sites in alignment...........: 148 288s Number of chars in alignment...........: 150876 288s Mean site entropy in alignment.........: 0.331041 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3202 1094 -17 149 +1 150055 -821 288s Number of sequences in alignment.......: 1094 288s Number of sites in alignment...........: 149 288s Number of chars in alignment...........: 150055 288s Mean site entropy in alignment.........: 0.325678 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3283 1034 -60 150 +1 144300 -5755 288s Number of sequences in alignment.......: 1034 288s Number of sites in alignment...........: 150 288s Number of chars in alignment...........: 144300 288s Mean site entropy in alignment.........: 0.310772 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3201 869 -165 151 +1 120684 -23616 288s Number of sequences in alignment.......: 869 288s Number of sites in alignment...........: 151 288s Number of chars in alignment...........: 120684 288s Mean site entropy in alignment.........: 0.320746 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 3206 867 -2 152 +1 121198 514 288s Number of sequences in alignment.......: 867 288s Number of sites in alignment...........: 152 288s Number of chars in alignment...........: 121198 288s Mean site entropy in alignment.........: 0.32085 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 2890 153 -714 157 +5 23971 -97227 288s Number of sequences in alignment.......: 153 288s Number of sites in alignment...........: 157 288s Number of chars in alignment...........: 23971 288s Mean site entropy in alignment.........: 0.0601394 288s Choice Node #seq %seq #sites %sites #chars %chars 288s 1) 1887 117 -36 158 +1 18405 -5566 288s Number of sequences in alignment.......: 117 288s Number of sites in alignment...........: 158 288s Number of chars in alignment...........: 18405 288s Mean site entropy in alignment.........: 0.0581426 288s Choice Node #seq %seq #sites %sites #chars %chars 288s BppAlnOpt's done. Bye. 288s Total execution time: 0.000000d, 0.000000h, 0.000000m, 9.000000s. 288s ****************************************************************** 288s * Bio++ Alignment Optimizer, version 1.1.0. * 288s * Author: J. Dutheil Last Modif. 14/03/18 * 288s * E. Figuet * 288s ****************************************************************** 288s 288s Parsing options: 288s Parsing file AlnOptimFasttreeStop.bpp for options. 288s Alphabet type .........................: Proteic 288s Sequence file .........................: PF01049_full.txt 288s Sequence format .......................: FASTA file 289s Minimum amount of data per site........: 0.7 289s Filter gap characters..................: yes 289s Filter unresolved characters...........: yes 289s Number of reference sequences..........: 0 289s Total number of sequences..............: 1652 289s Total number of sites..................: 656 289s Input tree file .......................: PF01049_fasttree.dnd 289s Input tree format .....................: Newick 289s Minimum number of sequences to keep....: 826 289s Comparison criterion:..................: MaxSites 289s Number of sequences in alignment.......: 1652 289s Number of sites in alignment...........: 129 289s Number of chars in alignment...........: 182603 289s Mean site entropy in alignment.........: 0.394104 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 2030 1647 -5 131 +2 184714 2111 289s Number of sequences in alignment.......: 1647 289s Number of sites in alignment...........: 131 289s Number of chars in alignment...........: 184714 289s Mean site entropy in alignment.........: 0.394129 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 1930 1645 -2 132 +1 185794 1080 289s Number of sequences in alignment.......: 1645 289s Number of sites in alignment...........: 132 289s Number of chars in alignment...........: 185794 289s Mean site entropy in alignment.........: 0.394195 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 1882 1644 -1 133 +1 186920 1126 289s Number of sequences in alignment.......: 1644 289s Number of sites in alignment...........: 133 289s Number of chars in alignment...........: 186920 289s Mean site entropy in alignment.........: 0.394263 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 386 1634 -10 134 +1 187634 714 289s Number of sequences in alignment.......: 1634 289s Number of sites in alignment...........: 134 289s Number of chars in alignment...........: 187634 289s Mean site entropy in alignment.........: 0.394887 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 357 1627 -7 135 +1 188437 803 289s Number of sequences in alignment.......: 1627 289s Number of sites in alignment...........: 135 289s Number of chars in alignment...........: 188437 289s Mean site entropy in alignment.........: 0.394741 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 1736 1614 -13 136 +1 188713 276 289s Number of sequences in alignment.......: 1614 289s Number of sites in alignment...........: 136 289s Number of chars in alignment...........: 188713 289s Mean site entropy in alignment.........: 0.394145 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 1489 1527 -87 137 +1 181488 -7225 289s Number of sequences in alignment.......: 1527 289s Number of sites in alignment...........: 137 289s Number of chars in alignment...........: 181488 289s Mean site entropy in alignment.........: 0.378687 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 2247 1524 -3 138 +1 182435 947 289s Number of sequences in alignment.......: 1524 289s Number of sites in alignment...........: 138 289s Number of chars in alignment...........: 182435 289s Mean site entropy in alignment.........: 0.378731 289s Choice Node #seq %seq #sites %sites #chars %chars 289s 1) 408 1515 -9 139 +1 183008 573 290s Number of sequences in alignment.......: 1515 290s Number of sites in alignment...........: 139 290s Number of chars in alignment...........: 183008 290s Mean site entropy in alignment.........: 0.377294 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 1819 1488 -27 140 +1 182208 -800 290s Number of sequences in alignment.......: 1488 290s Number of sites in alignment...........: 140 290s Number of chars in alignment...........: 182208 290s Mean site entropy in alignment.........: 0.374188 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 1676 1464 -24 141 +1 180695 -1513 290s Number of sequences in alignment.......: 1464 290s Number of sites in alignment...........: 141 290s Number of chars in alignment...........: 180695 290s Mean site entropy in alignment.........: 0.371696 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 416 1457 -7 142 +1 181323 628 290s Number of sequences in alignment.......: 1457 290s Number of sites in alignment...........: 142 290s Number of chars in alignment...........: 181323 290s Mean site entropy in alignment.........: 0.36917 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 1823 1371 -86 143 +1 176415 -4908 290s Number of sequences in alignment.......: 1371 290s Number of sites in alignment...........: 143 290s Number of chars in alignment...........: 176415 290s Mean site entropy in alignment.........: 0.359961 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 783 1355 -16 144 +1 175237 -1178 290s Number of sequences in alignment.......: 1355 290s Number of sites in alignment...........: 144 290s Number of chars in alignment...........: 175237 290s Mean site entropy in alignment.........: 0.360644 290s Choice Node #seq %seq #sites %sites #chars %chars 290s 1) 953 1307 -48 145 +1 169472 -5765 290s Number of sequences in alignment.......: 1307 290s Number of sites in alignment...........: 145 290s Number of chars in alignment...........: 169472 290s Mean site entropy in alignment.........: 0.363152 290s Choice Node #seq %seq #sites %sites #chars %chars 290s Output alignment file .................: PF01049_optimized_fastml.fasta 290s Output alignment format ...............: FASTA file 290s Output tree file ......................: PF01049_optimized_fastml.dnd 290s Output tree format ....................: Newick 290s BppAlnOpt's done. Bye. 290s Total execution time: 0.000000d, 0.000000h, 0.000000m, 2.000000s. 290s PASS 291s autopkgtest [21:20:46]: test run-unit-test: -----------------------] 291s run-unit-test PASS 291s autopkgtest [21:20:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 292s autopkgtest [21:20:47]: @@@@@@@@@@@@@@@@@@@@ summary 292s run-unit-test PASS 310s nova [W] Skipping flock for amd64 310s Creating nova instance adt-plucky-amd64-physamp-20250315-211554-juju-7f2275-prod-proposed-migration-environment-2-166de6a2-b886-45ca-a44c-2457749262f3 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 310s nova [W] Timed out waiting for 6c20b0cb-dab2-453c-8964-86ef2202a801 to get deleted.